Rename FASTA lookup helper: sequence_lookup_with_ens_fallback → lookup_sequence_with_version_fallback#352
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…on_fallback The old name was misleading: the fallback isn't to "ENS" (both Ensembl and GENCODE IDs start with ENS); the fallback is to a version-stripped form. The ENS prefix is just a safety gate so we don't strip non-Ensembl .N suffixes (e.g. TAIR isoform suffixes like AT1G01010.1). Docstring rewritten to reflect that both Ensembl and GENCODE produce versioned IDs - the formats just split that information differently (Ensembl in a separate *_version attribute, GENCODE embedded in the ID itself). The helper exists for the GENCODE case where the GTF stores the full versioned ID and a literal FASTA lookup would miss. No back-compat shim: this helper was added today in v2.9.6 and isn't exposed in __init__.py, so no external callers can depend on the old name. Bump version to 2.9.7.
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coverage: 84.971%. remained the same — rename-version-fallback-helper into main |
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Summary
The helper I added in #350 / v2.9.6 was misnamed. ENS isn't the fallback — both Ensembl and GENCODE protein/transcript IDs start with ENS. The actual fallback is to a version-stripped form of the same ID; the ENS-prefix check is just a guard that says "this ID has a version we know how to strip safely" (in contrast to e.g. TAIR
AT1G01010.1where.1is an isoform suffix, not a version).Renamed to
lookup_sequence_with_version_fallbackand the docstring is rewritten to correctly describe both Ensembl and GENCODE as having versioned IDs (they just split that information differently across the GTF / FASTA pair).Internal helper only — not exported from
pyensembl/__init__.py, was added today in v2.9.6, so no external callers can depend on the old name. No back-compat shim.Three call sites updated:
Transcript.sequenceTranscript.protein_sequenceGenome.transcript_sequence(id)/Genome.protein_sequence(id)Bumps version to 2.9.7.
Test plan
pytest tests/test_versioned_protein_fasta.py tests/test_mouse.py tests/test_tair10_complete.py tests/test_versions.py tests/test_sequence_data.py tests/test_transcript_sequences.py(20 passed locally)./lint.sh